[Publications]

 

Journal Papers



  1. F.Bai, Faruck Morcos, Y.S. Sohn, M. Darash-Yahana, C.O. Rezende, C.H. Lipper, M.L. Paddock, L. Song, Y. Luo,

S.H. Holt, S. Tamir, E.A. Theodorakis, P.A. Jennings, J.N. Onuchic, R. Mittler and R. Nechushtai. The Fe-S
cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer. Proceedings
of the National Academy of Science of the USA. Early Edition, 2015.

[Highlighted in Mammary Cell News]


  1. S.Tamir, M.L. Paddock, M. Darash-Yahana-Baram, S.H. Holt, Y.S. Sohn, L. Agranat, D. Michaeli, J.T. Stoeth, CH Lipper,

Faruck Morcos, I.Z. Cabantchik,  J.N. Onuchic, P.A. Jennings, R Mittler and R. Nechushtai. Structure-function

analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease.

Biochimica et Biophysica Acta (BBA) Molecular Cell Research. 2014 (In press)


Faruck Morcos, Nicholas P. Schafer, Ryan Cheng, Jose N. Onuchic and Peter G. Wolynes. Coevolutionary information,
protein folding landscapes, and the thermodynamics of natural selection. Proceedings of the National Academy of

Science of the USA. 111(34): 12408-12413,  2014. [Download] [ScienceNewsline]


  1. S.Tamir, S. Rotem-Bamberger, C. Katzb, F. Morcos, K.L. Hailey, J. A. Zuris, C. Wang, A.R. Conland, C.H. Lipper,

M.L. Paddock, R. Mittler, J.N. Onuchic, P.A. Jennings, A. Friedler and R Nechushtai. Integrated strategy reveals the

protein interface between cancer targets Bcl-2 and NAF-1. Proceedings of the National Academy of Science of the

USA. 111(14) 5177-5182, 2014 [Download]


Biman Jana, Faruck Morcos and Jose N. Onuchic. From Structure to Function: the Convergence of Structure Based

Models and Co-evolutionary Information. Physical Chemistry Chemical Physics. Vol. 16, No. 14, 6496-507, 2014

[Download]


Ryan Cheng, Faruck Morcos, Herbert Levine and José N. Onuchic. Towards rationally redesigning bacterial

two-component signaling systems using coevolutionary information. Proceedings of the National Academy of Science of

USA.  111(5): E563-71, 2014. [Download] [Phys.org] [technology.org] [ScienceDaily]

An NSF perspective on potential applications of this project: [NSF]


Faruck Morcos, Biman Jana, Terence Hwa and Jose N. Onuchic. Co-evolutionary signals across protein lineages help

capture multiple protein conformations. Proceedings of the National Academy of Science of the USA.

110(51):20533-20538, 2013. [Download] [ScienceDaily] [Rice University news]


Ramy Mourad, Zaher Dawy and Faruck Morcos. Designing Pooling Systems for Noisy High-Throughput Protein-Protein Interaction Experiments using Boolean Compressed Sensing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 10(6): 1478-1490, 2013.


Joanna I. Sulkowska*, Faruck Morcos*, Martin Weigt, Terence Hwa and Jose N. Onuchic. Genomics-aided structure prediction. Proceedings of the National Academy of Science of the USA, Vol. 109, No. 26, Pages 10340-45, 2012.

(*equivalent contribution) [Download] [ScienceDaily] [NSF news]


Faruck Morcos*, Andrea Pagnani*, Bryan Lunt, Arianna Bertolino, Debora S. Marks, Chris Sander, Riccardo Zecchina,
Jose N. Onuchic, Terence Hwa and Martin Weigt. Direct-coupling analysis of residue coevolution captures native contacts across many protein families.  Proceedings of the National Academy of Science of the USA, Vol. 108, No. 49,
E1293-E1301, 2011. (*equivalent contribution) [Download] [PDF] [Supplementary Information]


C. Harvey, Faruck Morcos, C. Sweet, D. Kaiser, S. Chatterjee, X. Liu, D. Chen and M. Alber. Study of elastic collisions
of Myxococcus xanthus in swarms. Physical Biology. Vol. 8, No. 2, 2011.  [Download]


Faruck Morcos, R. Lopez, S. Chatterjee, P. Brenner, C. McClendon, J. Zintsmaster, M. Ercsey-Ravasz, C.R. Sweet,
M. Jacobson, J. Peng and J. Izaguirre. Modeling conformational ensembles of slow functional motions in Pin1-WW.
PLoS Computational Biology. 2010. [Download]


Faruck Morcos, Marcin Sikora, Mark Alber, Dale Kaiser and Jesus A. Izaguirre. Belief Propagation Estimation of Protein and Domain Interactions using the Sum-Product Algorithm. IEEE Transactions on Information Theory, Special Issue on
Information Theory in Molecular Biology and Neuroscience. Vol. 56, No. 2, Pages 742-755, February, 2010.
[Download]


Zaher Dawy, Faruck Morcos, Johanna Weindl and Jakob C. Mueller. Translation initiation modeling and mutational
analysis based on the 3-end of the Escherichia coli 16S rRNA sequence. Elsevier BioSystems. 2009.  [Download]


Faruck Morcos, Charles Lamanna, Marcin Sikora and Jesus Izaguirre. Cytoprophet: a Cytoscape plug-in for the protein
and domain interaction networks inference. Bioinformatics, Vol. 24, Issue 19, Pages 2265-2266, July 2008.  [Download]


S. Flores, K. Keating, J. Painter, F. Morcos, K. Nguyen, E. Merrit, L. Kuhn and M. Gerstein. HingeMaster: normal mode
hinge prediction approach and integration of complementary predictors. Proteins: Structure, Function, and Bioinformatics. Vol. 73, Issue 2, Pages 299-319, Nov, 2008. [Download]


Zaher Dawy, Pavol Hanus, Johanna Weindl, Janis Dingel, Faruck Morcos. On genomic coding theory. European
Transactions on Telecommunications, John Wiley & Sons, Ltd. Vol. 18, Issue 8, Pages 873-879, Dec. 2007. 
[Download]


Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesus A. Izaguirre.

Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 4 pp. 78-87. Jan-March 2007.  [Download]


Book Chapters


Faruck Morcos, Terence Hwa, José N. Onuchic and Martin Weigt. Direct Coupling Analysis for protein contact prediction. Protein Structure Prediction, Methods in Molecular Biology, 3rd Edition. Springer Science+Business Media. 2014



Peer-reviewed Conference Papers


Faruck Morcos, Marcin Sikora, Dale Kaiser, Mark Alber and Jesus Izaguirre. Estimation of protein and domain interactions in the switching motility system of Myxococcus xanthus. Pacific Symposium of Biocomputing (PSB). 157-65, January, 2010. [Download]


Faruck Morcos, Charles Lamanna, Nitesh V. Chawla and Jesus Izaguirre. Determination of Specificity Residues in Two Component Systems using Graphlets. International Conference on Bioinformatics and Computational Biology
(BIOCOMP). July, 2009. [Download]


Marcin Sikora, Faruck Morcos, Daniel J. Costello, Jr., and Jesus A. Izaguirre. Bayesian Inference of Protein and Domain Interactions Using The Sum-Product Algorithm. Information Theory and Applications Workshop. UCSD, San Diego,
January 2007. [Download]


Faruck Morcos, Mike Boxem, Niels Klitgord, Marc Vidal, and Jesus A. Izaguirre. Prediction of domain interactions in C.
elegans. Proc. Workshop Computational Biophysics to Systems Biology CBSB06, Forschungszentrum Julich, Germany, June 2006. [Download]


Faruck Morcos, Thidapat Chantem, Philip Little, Tiago Gasiba, and Douglas Thain. iDIBS: An Improved Distributed
Backup System. IEEE Conference on Parallel and Distributed Systems (ICPADS), Minneapolis MN, July 2006.
[Download]


Zaher Dawy, Faruck Morcos González, Joachim Hagenauer and Jakob C. Muller. Modeling and Analysis of Gene
Expression Mechanisms: A Communication Theory Approach . IEEE International Conference on Communications.
Seoul, Korea, 16-20 May, 2005. [Download]


Pedro Tejera, Mario Castaneda, Faruck Morcos and Wolfgang Utschick. Degradation and Performance Issues of
MIMO/OFDM in the Presence of Motion. Proceedings of IEEE Vehicular Technology Conference. Milan, Italy, May 17-19, 2004. [Download]


Presentations & Conferences


  1. -The role of coevolutionary information in the study of protein structure and association. Significance of Knotted
    Structures for Functions in Proteins and Nucleic Acids , Warsaw, Poland, September 2014 (talk)


  1. - A relationship between coevolutionary information, folding landscapes and the thermodynamics of natural
    sequence selection.     Significance of Knotted Structures for Functions in Proteins and Nucleic Acids, Warsaw,
    Poland, September 2014 (poster)


  1. -A relationship between coevolutionary information, folding landscapes and the thermodynamics of natural
    sequence selection.     Zing Conference on Protein Folding, Punta Cana, Dominican Republic. July, 2014 (invited talk)


  1. -Uncovering protein structural diversity and protein recognition in signaling pathways using coevolutionary information.

  ICM Seminar, Uppsala University, Uppsala, Sweden. April, 2014 (invited talk)

  1. - Uncovering protein structural diversity and protein recognition in signaling pathways using coevolutionary information.

  University of Warsaw, Warsaw, Poland. April, 2014 (invited talk)


  1. -Exploring co-evolutionary information to uncover amino acid interactions, protein structure, complex formation and conformational plasticity. 5th Meeting on Molecular Simulations: from simple fluids to chemical reactions. Mexico City,
    Mexico, December, 2013 (invited talk).


  1. -Conformational changes leave an evolutionary footprint across protein lineages. Zing Protein/RNA Structure Prediction Conference, Riviera Maya, Mexico. December, 2013 (talk)


  1. -Conformational changes leave an evolutionary footprint across protein lineages. GRC Proteins Conference, Holderness, NH. June, 2013 (poster).


- Large Scale Direct Coupling Analysis of Residue-Residue Co-evolution Reveals Native Contacts in Many Domain Families. Dept. of Chemistry and Biochemistry Seminar Series at California State University Long Beach. February, 2012 (invited talk).


  1. -Folding with incomplete information. GRC Protein Folding Conference, Ventura, CA. Jan, 2012 (poster)


  1. -Large Scale Direct Coupling Analysis of Residue-Residue Co-evolution Reveals Native Contacts in Many Domain
    Families.     Zing Conference on Protein and RNA structure prediction, Cancun, Dec, 2011 (talk)


  1. -Fast Identification of directly co-evolving residues in large protein families. San Diego Microbiology Group Annual
    Meeting. San Diego, May, 2011 (talk)


- Determination of Specificity Residues in Two Component Systems using Graphlets. International Conference on
Bioinformatics and Computational Biology (BIOCOMP). Las Vegas, July, 2009 (talk)


- Protein and domain interaction inference in the switching motility system of Myxococcus xanthus using Cytoprophet. International Conference on Systems Biology. Gothenburg, Sweden. August, 2008 (poster)


- Simulating reversals in swarming and fruiting body formation in Myxococcus Xanthus and implications for genetic modification. Indy Bioinformatics Conference. UIPU, Indianapolis, IN. June, 2007 (poster)


  1. -Refining Protein-Protein Docking with Domain-Domain Interaction Predictions. Biomedical Engineering Society Annual

Meeting. Chicago, IL, October, 2006. (talk)


  1. -Proteome (in silico) analysis of Virulence Factors in organisms M. Tuberculosis, N. Farcinica, and M. Leprae

XXIII National Congress of Biomedical Research. Monterrey, Mexico, October , 2005. (In Spanish)


- Degradation and Performance Issues of MIMO/OFDM in the Presence of Motion. Vehicular Technology Conference.
Milan, Italy, May , 2004.

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